VMD-L Mailing List

From: Yasser Almeida-Hernandez (yasser.almeida-hernandez_at_uni-due.de)
Date: Mon Aug 03 2020 - 09:46:12 CDT

 

Hi JC,

I tried one of the 1.9.4 alpha with two molecules. Again, when hitting
'Run optimization' nothing happens except that it writes the TCL script.
When the script is executed in the Tk console, it raises an error:

Action halted on error!
The following QM output file was not recognized:

I used Gaussian G09 for the hessian calculation.

Any thought?

Yasser

On 03.08.2020 16:28, JC Gumbart wrote:
> Can you try using one of the latest 1.9.4 alpha builds and see if the
> problem still occurs?
>
> Best,
> JC
>
>> On Aug 3, 2020, at 7:46 AM, Yasser Almeida-Hernandez
>> <yasser.almeida-hernandez_at_uni-due.de> wrote:
>>
>> Hello,
>>
>> I am optimizing 2 angles in a molecule (VMD for LINUXAMD64, version
>> 1.9.3). After filling all fields and hit 'Run optimization' nothing
>> happens. I generated the TCL script, and when executed, it runs
>> apparently OK but the end of the BondedOpt.debug.log ends with:
>>
>> NAMD run complete
>>
>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>
>> DONE
>> downhill: optimization -downhill -tol 0.001 -iter 500 -function
>> ::ForceFieldToolKit::BondAngleOpt::optBondsAngles
>>
>> Raw Result: {45 109 45 109} 0.0
>>
>> DONE
>>
>> The BondedOpt.log is:
>>
>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>
>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>
>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>
>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>
>> Current objective value: 0.000000 ( En: 0.000000 Geom: 0.000000 )
>>
>> FINAL PARAMETERS
>> angle {CG2O5 CG321 OG301} 45.0000 109.0000
>> angle {CG2O5 CG321 OG303} 45.0000 109.0000
>> END
>>
>> ... so no angle is optimized, since those are the initial values. I
>> set those as initial and repeated but got the ame result.
>>
>> Also in the VMD terminal it states:
>>
>> ERROR) Invalid last frame: 1
>> Info) Using plugin namdbin for coordinates from file
>> min-bondangles.coor
>> Info) Finished with coordinate file min-bondangles.coor.
>> Info) Opened coordinate file namd-temp.pdb for writing.
>> Info) Finished with coordinate file namd-temp.pdb.
>> Info) Opened coordinate file namd-temp.dcd for writing.
>> Info) Finished with coordinate file namd-temp.dcd.
>> ERROR) Invalid last frame: 1
>> Info) Using plugin namdbin for coordinates from file
>> min-bondangles.coor
>> Info) Finished with coordinate file min-bondangles.coor.
>> Info) Opened coordinate file namd-temp.pdb for writing.
>> Info) Finished with coordinate file namd-temp.pdb.
>> Info) Opened coordinate file namd-temp.dcd for writing.
>> Info) Finished with coordinate file namd-temp.dcd.
>> ERROR) Invalid last frame: 1
>> Info) Using plugin namdbin for coordinates from file
>> min-bondangles.coor
>> Info) Finished with coordinate file min-bondangles.coor.
>> Info) Opened coordinate file namd-temp.pdb for writing.
>> Info) Finished with coordinate file namd-temp.pdb.
>> Info) Opened coordinate file namd-temp.dcd for writing.
>> Info) Finished with coordinate file namd-temp.dcd.
>> ERROR) Invalid last frame: 1
>> Info) Using plugin namdbin for coordinates from file
>> min-bondangles.coor
>> Info) Finished with coordinate file min-bondangles.coor.
>> Info) Opened coordinate file namd-temp.pdb for writing.
>> Info) Finished with coordinate file namd-temp.pdb.
>> Info) Opened coordinate file namd-temp.dcd for writing.
>> Info) Finished with coordinate file namd-temp.dcd.
>> ERROR) Invalid last frame: 1
>>
>> What ERROR) Invalid last frame: 1 means? I read the thread
>> https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html
>> [1] but was not very helpful.
>>
>> Any help or advice with this issue will be very much appreciated
>> since I have been stuck with this since a while.
>>
>> Best,
>> Yasser
>>
>> --
>> Dr. Yasser Almeida-Hernandez
>> Postdoctoral Researcher
>> Computational Biochemistry
>> T03 R01 D45
>> Faculty of Biology
>> University of Duisburg-Essen
>> Universitätsstr. 2, 45117 Essen
>> Email: yasser.almeida-hernandez_at_uni-due.de
>> Phone: +49 201 183 2457
>
>
>
> Links:
> ------
> [1] https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22497.html